46 lines
1.7 KiB
Markdown
46 lines
1.7 KiB
Markdown
Free Energy of Hydration of SPCE Water
|
|
======================================
|
|
|
|
Example calculation of the free energy of hydration of water with
|
|
LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/soft*.
|
|
|
|
The Lennard-Jones sites and the electrostatic charges are
|
|
created/annihilated in separate runs, which simplifies the use of
|
|
*fix adapt/fep* and *compute fep*. The Lennard-Jones sites are handled
|
|
using soft core potentials (*pair lj/cut/soft*). Trajectories are at
|
|
constant NpT, so corrections for the fluctuating volume are included.
|
|
|
|
The following directories contain input files and results for
|
|
calculations using free-energy perturbation (FEP):
|
|
|
|
* `mols` -- molecule description files and force field database used
|
|
to create the initial configuration used for the simulations
|
|
`data.lmp`
|
|
|
|
* `fep01` -- Calculation using FEP, multi-stage creation of one SPC/E
|
|
molecule, LJ and q. Results in `fep01-lj.fep` and `fep01-lj.fep`
|
|
|
|
* `fep10` -- Calculation using FEP, multi-stage deletion of one SPC/E
|
|
molecule, q and LJ. Results in `fep10-q.fep` and `fep10-lj.fep`
|
|
|
|
The Python script `fep.py` found in the
|
|
`tools` directory can be used to calculate the free-energy differences
|
|
corresponding to the transformations above:
|
|
|
|
fep.py 300 < fep01-lj.fep
|
|
|
|
fep.py 300 < fep01-q.fep
|
|
|
|
fep.py 300 < fep10-q.fep
|
|
|
|
fep.py 300 < fep10-lj.fep
|
|
|
|
The outputs are in kcal/mol and can be compared with the experimental
|
|
value of -6.3 kcal/mol, or with a simulation value from the literature
|
|
of -6.7 kcal/mol
|
|
[Gonçalves, Stassen, Pure Appl Chem 76 (2004) 231](https://doi.org/10.1351/pac200476010231).
|
|
|
|
These example calculations are for tutorial purposes only. The results
|
|
may not be of research quality (not enough sampling, size of the step
|
|
in lambda not optimized, etc.)
|